Practical Course

European Molecular Biology Organization

 

Computational molecular evolution

29 April - 10 May 2012 | Heraklion | Greece

Instructors

 

Maria Anisimova
ETH Zurich, Switzerland

Maria Anisimova is a senior research fellow at the Computational Biochemistry Research group headed by Prof Gaston Gonnet and a lecturer at the Institute of Computational Science of the Federal Swiss Institute of Technology (ETH Zürich):www.inf.ethz.ch/personal/anmaria. Maria has an undergraduate degree in pure Mathematics from the Pedagogical State University of Nizhny Novgorod, Russia. After teaching Geometry and Mathematics for Finance and Business in London, she obtained an MRes in modeling biological complexity (CoMPLEX) and a PhD in statistical genomics under the supervision of Prof Ziheng Yang (Biology department) at University College London. During her PhD Maria worked on methods for detecting adaptive evolution on the protein-coding genes. Postdoctoral work included large-scale data analyses of viral and bacterial genomes with Prof Yang and statistical tests for clade supports with Prof Olivier Gascuel (LIRMM) at Université Montpellier II, France. Maria's current research interests involve stochastic modeling of molecular evolution, statistical testing in phylogenetics and the application of machine leaning techniques to large complex biological data.

Aglaia (Cilia) Antoniou
Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, Greece

Aglaia Antoniou is a postdoctoral researcher at the Institute of Marine Biology and Genetics (HCMR; http://www.hcmr.gr/listview3.php?id=35). She is a biologist with a long-time interest in Evolutionary Biology, especially in the field of Population and Landscape Genetics, Phylogenetics, and Phylogeography. In 2008, she received a PhD in population and landscape genetics from the Biology Department of the University of Crete, Greece. Her current research focuses on the landscape genetics of marine animals by merging population genetics and phylogenetic approaches in space and time.

Simon Berger
Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany

Simon Berger is a PhD student in Alexandros Stamatakis's group at the Heidelberg Institute for Theoretical Studies (HITS). Simon studied bioinformatics at the Technical University and Ludwig Maximilian University in Munich, Germany. His PhD project is focused on the analysis of short sequence reads in a phylogenetic context. One main goal is to develop scalable tools for adding new sequence reads to existing reference alignments, and for establishing their provenance relative to a fixed reference phylogeny. Simon is co-developer of PaPaRa (phylogeny aware short read alignment algorithm) and EPA (Evolutionary Placement Algorithm, part of RAxML).

Aidan Budd
European Molecular Biology Laboratory (EMBL), Germany

Aidan Budd is a member of staff at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, where he works as a computational biologist in the group of Toby Gibson. He is interested in the evolution and prediction of short protein linear motifs, and in the evolution of individual gene families. Additionally, Aidan is involved in teaching and organising practical courses for researchers, mostly focusing on multiple sequence alignment, phylogenetics, and exploration of protein modular architecture - along with introductory courses for secondary school teachers in bioinformatics.

After studying for his undergraduate degree in Zoology at Cambridge University, Aidan worked as a research assistant with Torsten Krude in the lab of Ron Laskey at the Gurdon Institute in Cambridge. He went on to obtain his PhD at EMBL Heidelberg focusing on the evolution of gene families expected to have similar evolutionary histories. Between completing his PhD and rejoining EMBL, Aidan worked as the commissioning editor for life science books at Wiley-VCH in Weinheim, Germany.

Martin Embley
Institute for Cell and Molecular Bioscience, Medical School, Newcastle University, UK

Martin Embley is Professor of Molecular Evolution at Newcastle University. His current and long-term research interests are on the early evolution of eukaryotes and the evolution and functions of their organelles, particularly of mitosomes and hydrogenosomes. These are peculiar forms of mitochondria found in anaerobic and obligate intracellular parasitic protists. His lab also participated in the analysis of lateral gene transfer as it affects the genomes of major protozoan parasites.

Prof. Embley is an Associate Editor of Genome Biology and Evolution, a Fellow of the American Academy of Microbiology, a Royal Society Wolfson Research Merit award holder and a Member of the European Molecular Biology Organisation.

Olivier Gascuel
The Montpellier Laboratory of Computer Science, Robotics, and Microelectronics, France

Olivier Gascuel first studied mathematics although his PhD was in computer science, and he started working in bioinformatics in the 80's, at the very beginning of the genomic era and of the rapid development of interactions between mathematicians, computer scientists and molecular biologists. His first interests were in sequence analysis and protein structure prediction, using machine learning approaches. Since the mid-90's, Olivier Gascuel has concentrated on evolution and phylogenetics, with particular focus on the mathematical and computational tools and concepts. He now leads a research group at the Centre National de la Recherche Scientifique, Montpellier (France). He is an associate editor of Systematic Biology and belongs to the editorial board of several bioinformatics journals. He has published 120 papers and book chapters, and authored several widely used computer programs in phylogenetics and bioinformatics. He has recently started a new adventure fighting pathogens, (HIV, malaria, leishmania...), especially in Africa and endemic countries.

Nick Goldman
EMBL - European Bioinformatics Institute, UK

Nick Goldman is a Research Group Leader at the EMBLEuropean Bioinformatics Institute (EBI) in Hinxton, UK, where his research group studies methods for the analysis of DNA and amino acid sequences to study evolution. Nick studied Mathematics at the University of Cambridge, and has a PhD on statistical methods for studying sequence evolution. He worked at the Natural History Museum, London, the MRC National Institute for Medical Research, London, and the Departments of Genetics and Zoology, Cambridge, before joining EBI in 2002. Contributions to molecular evolution include papers on various statistical methods in phylogenetics, codon models to describe the evolution of protein-coding DNA, the relationships between protein sequence and structure, experimental design in phylogenetics, evolutionary multiple sequence alignment and various large-scale comparative genomics projects. Further information is available at www.ebi.ac.uk/goldman.

John Huelsenbeck
UC Berkeley, USA

John Huelsenbeck is a Professor of Integrative Biology at the University of California, Berkeley. He received his Ph.D. in Zoology from the University of Texas at Austin in 1995.

His research interests are in theoretical phylogenetics and molecular evolution. He is a coauthor of the program MrBayes, a program that is widely used for the Bayesian estimation of phylogeny.

Carolin Kosiol
Institute of Population Genetics, Vetmeduni Vienna, Austria

Carolin Kosiol is a junior research group leader in the Institute of Population Genetics at the Vetmeduni Vienna, Austria. In 2006, she received a PhD from the European Bioinformatics Institute and the University of Cambridge. She then pursued a postdoc at Cornell University working to the detection of natural selection and conducted various inter- and intraspecific signatures of selection in mammals. Recently, she was involved in several genome projects, e.g., rhesus macaque, giant panda bear and orangutan. Her main interest is to study the evolutionary processes and pressures acting on molecular sequences by merging population genetic and phylogenetic approaches.

Clemens Lakner
Bioinformatics Research Center, North Carolina State University, USA

Clemens is a postdoc at the Bioinformatics Research Center at North Carolina State University (NCSU). His advisors at NCSU are Jeff Thorne and Eric Stone. Clemens is interested in questions relating to protein evolution and in developing computational approaches to address them. After studying biology in Vienna, he obtained a doctoral degree from Florida State University. For his PhD project Clemens evaluated stochastic models of protein evolution and implemented models that explicitly incorporate protein structural information.

Adam Leaché
Department of Biology & Burke Museum, University of Washington, USA

Adam Leaché is an Assistant Professor in the Department of Biology at the University of Washington, and the Curator of Genetic Resources and Herpetology at the Burke Museum of Natural History and Culture. Research in his lab is focused on the evolutionary biology and systematics of amphibians and reptiles. Topics of interest include species tree inference, statistical phylogeography, Bayesian species delimitation, and comparative biology.

Adam received his PhD from the University of California, Berkeley in 2008, where he worked in the Museum of Vertebrate Zoology studying speciation, phylogeography, and hybridization in North American lizards. He received an NSF Bioinformatics Postdoctoral Research Fellowship and worked with Bruce Rannala on statistical aspects of species tree inference and species delimitation. Further information is available at faculty.washington.edu/leache/wordpress.

Brian Moore
UC Davis, USA

My primary research interests focus on developing quantitative methods for phylogeny estimation and for making phylogenybased inferences related to various evolutionary processes (particularly inference problems associated with differential rates of lineage diversification and historical biogeography), exploring the statistical behavior of these methods via simulation, and applying them to empirical data to explore fundamental evolutionary problems in flowering plant evolution.

Sarah Parks
European Bioinformatics Institute, Hinxton, UK

Sarah Parks is a PhD student in Nick Goldman's group at the EBI. She obtained an undergraduate degree in Mathematics from the University of Cambridge and then completed a Masters in Computational Biology. Her research focuses on theoretical phylogenetics.

Pavlos Pavlidis
Heidelberg Institute for Theoretical Studies, DE

Pavlos is a postdoctoral researcher at the Exelixis Group headed by Alexandros Stamatakis at Heidelberg Institute for Theoretical Studies (HITS). Pavlos has studied Agricultural Biotechnology at the Agricultural University of Athens, Greece. He obtained his M.Sc. degree in Molecular Biology and Biotechnology at the University of Crete, Greece. He was a PhD student at the group of Wolfgang Stephan at LMU, Munich, Germany. During his PhD he studied selective sweeps in natural populations of Drosophila melanogaster, focusing on disentangling demography from selection. His current research at the Exelixis Group focuses on estimating the number of species from a sample of DNA sequences. Furthermore, he develops algorithms to detect positive selection in large datasets.

William R. Pearson
Dept. of Biochemistry and Molecular Genetics, University of Virginia, USA

Bill Pearson is a Professor of Biochemistry and Molecular Genetics at the University of Virginia. He obtained his undergraduate degree in Chemistry at the U. of Illinois, and did graduate work in Biochemistry and Molecular Biology at the California Institute of Technology. After post-doctoral fellowships at the Caltech Marine Station and John Hopkins School of Medicine, he became an Assistant Professor at the University of Virginia in 1983. Shortly there after, in collaboration with David Lipman, he wrote the FASTP program (1985), which evolved in to the FASTA program (1988). Dr. Pearson has continued to work on problems in protein evolution and biological sequence analysis, developing improved similarity searching methods and investigating the biological constraints on sequences and structures and the statistical relationships used to infer homology.

Bruce Rannala
Genome Center and Department of Evolution and Ecology, University of California, USA

Bruce Rannala is currently a Professor in the Genome Center and Department of Evolution and Ecology at UC Davis. He previously held positions on the faculty of SUNY Stony Brook and the University of Alberta and is currently a guest professor at the Chinese Academy of Sciences, Beijing and at Chiang Mai University, Thailand. In 2001, he was the Canadian Institutes of Health Research Peter Lougheed Scholar and in 2009 he was appointed as a Miller Professor at UC Berkeley.
Bruce Rannala's principal research interests include statistical aspects of population genetics and phylogenetic inference. He made early contributions to the development of Bayesian methods for phylogenetic inference, population genetic inference of fine-scale recombination rates and ages of mutations, and individual-based assignment methods and migration rate inference. Bruce Rannala received a B.Sc. in Zoology from the University of British Columbia in 1989 and a Ph.D. in Biology from Yale University in 1995. He was an NSERC postdoctoral fellow at UC Berkeley.

Benjamin Redelings
National Evolutionary Synthesis Center, North Carolina, USA

Benjamin Redelings is a postdoc at the National Evolutionary Synthesis Center (NESCent) in in Durham, NC. Ben is interested in mathematical models of protein sequence evolution, and hopes to make them more biologically realistic while remaining computationally tractable for estimating evolutionary trees. He has focused on Bayesian methods for estimating multiple sequence alignments and phylogenetic trees via MCMC. He received his Ph.D. in 2006 from the Biomathematics Department at UCLA. www.duke.edu/~br51

Antonis Rokas
Department of Biological Sciences, Vanderbilt University, USA

Antonis Rokas in an Assistant Professor of Biological Sciences at Vanderbilt University. He received his Ph.D. in 2001 from Edinburgh University for research on the evolutionary ecology of oak-feeding gallwasps. Before joining Vanderbilt, he worked at the Broad Institute of MIT and Harvard as a Research Scientist, and at the University of Wisconsin-Madison as a postdoctoral fellow. Research in the Rokas lab combines computational and experimental approaches to investigate the factors influencing phylogenetic accuracy and their usefulness in obtaining more robust phylogenies, the molecular origins of multicellularity in fungi and animals, and the molecular foundations of the fungal lifestyle. Further information is available at as.vanderbilt.edu/rokaslab

Alexandros Stamatakis
Heidelberg Institute for Theoretical Studies, Germany

Alexandros (Alexis) Stamatakis is currently the group leader of the scientific computing group at the Heidelberg Institute for Theoretical Studies (HITS gGmbH). He received a PhD in Computer Science from the Technical University of Munich in 2004. His research focus is on tools, algorithms, emerging parallel architectures, and high performance computing for evolutionary biology. Alexis is the main developer of RAxML, a code for largescale phylogeny reconstruction under Maximum Likelihood.

Jeff Thorne
Genetics and Statistics Departments, North Carolina State University, USA

Jeff Thorne is a professor in the Genetics and Statistics Departments of North Carolina State University. He was born in 1963 and spent most of his childhood in Wisconsin. His undergraduate degrees were in Molecular Biology and in Mathematics (University of Wisconsin, Madison). In 1991, he received a Ph.D. in Genetics from the University of Washington. His research concentrates on the development of statistical techniques for studying DNA sequence evolution. - Address: 311 Ricks Hall, Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695-7566, USA. E-mail: thorne@statgen.ncsu.edu

Ziheng Yang
Department of Genetics, Evolution and Environment, University College London, UK

Ziheng Yang is RA Fisher Professor of Statistical Genetics in University College London. After finishing his Ph. D. in Beijing Agricultural University, he worked as a postdoctoral researcher in Cambridge, London, and the USA, before taking up a faculty position in UCL in 1997. He was elected a fellow of the Royal Society in 2006. He develops statistical models and write computer programs for comparative analysis of DNA and protein sequence data in molecular evolution, molecular systematics, and population genetics. His contributions includes models of variable rates among sites, likelihood method of ancestral reconstruction, codon models, Bayesian methods of phylogeny reconstruction and divergence time estimation, partition and mixed models for analysing multi-gene datasets, and Bayesian computational analysis of phylogeographic data under the coalescent model. He maintains a computer program package called PAML. He published >100 papers and a book titled Computational Molecular Evolution (Oxford, 2006). Further information about his research is available at abacus.gene.ucl.ac.uk.

 

 

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